Plaques of amyloid β peptide (Aβ) are a hallmark trait of Alzheimer’s disease (AD). However, the precise role of Aβ aggregates is not well understood. Recent studies have identified that naturally occurring N-terminal truncation and pyroglutamylation of Aβ significantly increases its neurotoxicity by an unknown mechanism. Content of pyroglutamylated Aβ (pE-Aβ) in AD brains has been shown to reach up to 50% of total Aβ. Modified pE-Aβ co-aggregates with Aβ by a seeding mechanism and forms structurally distinct and highly toxic oligomers. We studied structural transitions of the full-length Aβ1-42, its pyroglutamylated form AβpE3-42, their 9:1 (Aβ1-42/AβpE3-42) and 1:1 molar combinations. Transmission electron microscopy was used to directly visualize the fibrils of the samples in a buffer mimicking physiological environment. Atomic force microscopy measurements were done to determine rate of second nucleation events in fibrils. Thioflavin-T fluorescence indicated that low ionic strength suppressed the aggregation of AβpE3-42 but promoted that of Aβ1-42, suggesting different paths of fibrillogenesis of unmodified Aβ and pE- Aβ. Interestingly, AβpE3-42 at only 10% significantly facilitated the fibrillization of Aβ1-42 at near-physiological ionic strength but had little effect at low salt. Circular dichroism and Fourier transform infrared (FTIR) spectroscopy were used to characterize the structural transitions during fibrillogenesis. In aqueous buffer, both unmodified Aβ and pE-Aβ peptides adopted parallel intermolecular β-structure. Interestingly, AβpE3-42 contained lower β-sheet content than 13C-Aβ1-42, while retaining significantly larger fractions of α-helical and turn structures. Structural details of Aβ and pE-Aβ combinations were unveiled by isotope-edited FTIR spectroscopy, using 13C-labeled Aβ1-42 and unlabeled AβpE3-42. When exposed to environmental humidity, AβpE3-42 not only maintained an increased fraction of α-helix but also was able to reverse 13C-Aβ1-42 β-sheet structure. These data provide a novel structural mechanism for pE-Aβ hypertoxicity; pE-Aβ undergoes faster nucleation due to its increased hydrophobicity, thus promoting formation of smaller, hypertoxic oligomers of partial α-helical structure.